Biochemical Pathways Workbench

加州大学圣地亚哥分校获得了一项资助，用于开发生物网络的综合通路数据库、查询/分析工具包、接口基础设施和创作工具包，称为生化通路工作台（BPW）。这个工作台的目标是为科学家提供一个计算沙箱，他们可以在其中开发复杂的应用程序，或者从数据库提供的大量分析工具中进行选择。该项目的目标是在生物建模、算法设计、分析建模、统计验证和部署到现有的生物学工作台（http://workbench.sdsc.edu）方面做出基本贡献。该项目将与普渡大学合作。传统的数据存储库为基于序列和结构的注释提供接口。鉴于生物学向通路、网络和系统发展的新趋势，有必要为通路提供数据、分析和建模接口。我们将为来自生化途径的各种数据源提供这样的接口，并使用我们自己实验室的数据和应用程序来增强这些数据源。该工具将提供与其他数据源（包括序列和表达式数据库）的互操作性，支持一个API，程序员可以使用该API透明地查询远程数据库，并以创作工具包的形式为其分析工具提供图形界面。使用该工具包，科学家将能够对集成到BPW网络和数据库中的各种数据源进行实验。开放架构中的基础设施将集成到生化途径工作台中，并提供给更广泛的科学和教育界。该项目将在第二年投入大量精力，在加州大学圣地亚哥分校和普渡大学开发教学媒体课程，以展示该工具的教育价值。

The University of California-San Diego is awarded a grant to develop a comprehensive pathways database, query/analysis toolkit, interface infrastructure, and an authoring toolkit, called Biochemical Pathways Workbench (BPW) for biological networks. The goal of this Workbench is to provide scientists with a computational sandbox in which they can develop complex applications, or choose from an extensive set of analysis tools provided by the database. The project targets fundamental contributions in biological modeling, algorithm design, analytical modeling, statistical validation, and deployment into the existing Biology Workbench (http://workbench.sdsc.edu). The project will be a collaborative effort with Purdue University.Traditional data repositories provide interfaces to sequence and structure-based annotations. Given the emerging trend in biology towards pathways, networks, and systems, there is a need to provide data, analysis, and modeling interfaces to pathways. We will provide such an interface to various data sources from biochemical pathways and enhance these with data and applications from our own laboratory. The tool will offer interoperability with other data sources including sequence and expression databases, support an API using which programmers will be able to transparently query remote databases, and provide a graphical interface to its analysis tools in the form of an authoring toolkit. Using this toolkit, scientists will be able to experiment with diverse data sources integrated into BPW networks and databases. The infrastructure in an open architecture will be integrated into the Biochemical Pathways WorkBench, and made available to the broader science and education community. The project will invest considerable effort during the second year to develop instructional media courses at UCSD and Purdue that demonstrate the educational value of the tool.